Table 3.
Transcription Factor Binding Sites Overrepresented in Up- and Down-regulated genes
| Downregulated gene set | Frequency (sites/1000bp) | |||||
| Matrix name | Transcription factor | Down | Background | Ratio | FDR | Matched promoters FDR |
| V$CDP_03 | Cutl1, CUX1, Cux1 | 0.74 | 0.15 | 4.82 | 5.6E-12 | 2.3E-05 |
| V$RORA_Q4 | Rora, RORA | 0.25 | 0.04 | 7.05 | 4.8E-06 | 5.2E-04 |
| V$OCT1_03 | POU2F1, Pou2f1, Pou2f1 | 0.43 | 0.11 | 3.91 | 3.5E-06 | 8.8E-04 |
| V$HMGA2_01 | Hmga2, HMGA2 | 0.38 | 0.10 | 3.97 | 1.1E-05 | 2.0E-03 |
| V$TAL1BETAE47_01 | Tal1, TAL1, Tcf3, TCF3, Tcf4, Tcf4, TCF4, Tcfe2a | 0.29 | 0.09 | 3.25 | 6.2E-04 | 3.4E-03 |
| V$OCT1_06 | POU2F1, Pou2f1, Pou2f1 | 0.42 | 0.11 | 3.74 | 9.1E-06 | 4.7E-03 |
| V$NKX61_03 | Nkx6-1, Nkx6-1, NKX6-1 | 0.27 | 0.07 | 4.17 | 1.4E-04 | 4.7E-03 |
| V$PBX1_04 | Pbx1, Pbx1, PBX1 | 0.27 | 0.08 | 3.61 | 4.2E-04 | 5.1E-03 |
| V$BRN2_01 | Pou3f2, POU3F2, Pou3f2 | 0.22 | 0.05 | 4.53 | 3.7E-04 | 5.3E-03 |
| V$SATB1_Q3 | SATB1, Satb1 | 0.25 | 0.07 | 3.44 | 8.9E-04 | 7.2E-03 |
| V$STAT5A_02 | Stat1, STAT1, Stat2, Stat2, STAT2, Stat3, STAT3, Stat3, Stat4, Stat4, STAT4, Stat4, Stat5a, Stat5a, STAT5A, Stat5b, STAT5B, Stat5b, Stat6, STAT6, Stat6 | 0.40 | 0.13 | 3.10 | 1.1E-04 | 8.6E-03 |
| V$TAL1ALPHAE47_01 | Tal1, TAL1, Tcf3, TCF3, TCF4, Tcf4, Tcf4, Tcfe2a | 0.24 | 0.08 | 3.12 | 2.4E-03 | 8.6E-03 |
| V$CEBPG_Q6_01 | CEBPG, Cebpg, Cebpg | 0.20 | 0.06 | 3.42 | 3.0E-03 | 0.011 |
| V$ATF5_01 | Atf5, Atf5, ATF5 | 0.20 | 0.07 | 3.06 | 5.4E-03 | 0.013 |
| V$HOX13_02 | HOXA5, Hoxa5, Hoxa5, Irf6, IRF6, Irf6 | 0.27 | 0.07 | 3.97 | 2.1E-04 | 0.014 |
| V$NKX61_02 | Nkx6-1, Nkx6-1, NKX6-1 | 0.18 | 0.04 | 5.04 | 6.4E-04 | 0.014 |
| V$POU6F1_03 | POU6F1, Pou6f1, Pou6f1 | 0.24 | 0.05 | 4.44 | 2.5E-04 | 0.014 |
| V$RORA2_01 | Rora, RORA | 0.20 | 0.04 | 4.47 | 6.8E-04 | 0.015 |
| V$CEBPA_01 | CEBPA, Cebpa, Cebpa, Cebpb, Cebpb, CEBPB | 0.18 | 0.05 | 3.78 | 2.8E-03 | 0.016 |
| V$HELIOSA_01 | IKZF1, Ikzf1, Ikzf2, IKZF2 | 0.18 | 0.05 | 3.78 | 2.8E-03 | 0.016 |
| V$BCL6_02 | BCL6, Bcl6, Bcl6 | 0.20 | 0.06 | 3.53 | 2.6E-03 | 0.016 |
| V$POU6F1_02 | Pou6f1, POU6F1, Pou6f1 | 0.25 | 0.06 | 4.35 | 1.7E-04 | 0.018 |
| V$SEF1_C | n/a | 0.18 | 0.06 | 3.02 | 8.2E-03 | 0.018 |
| V$CEBPB_Q6 | Cebpb, Cebpb, CEBPB | 0.20 | 0.05 | 3.88 | 1.5E-03 | 0.018 |
| V$CEBPB_01 | CEBPA, Cebpa, Cebpa, Cebpb, Cebpb, CEBPB | 0.38 | 0.13 | 3.00 | 2.2E-04 | 0.019 |
| V$SATB1_01 | n/a | 0.25 | 0.06 | 4.11 | 2.5E-04 | 0.019 |
| V$LHX3_01 | Lhx3, LHX3, Lhx3 | 0.42 | 0.12 | 3.43 | 2.5E-05 | 0.019 |
| V$STAT1STAT1_Q3 | Stat1, STAT1, Stat4 | 0.25 | 0.05 | 4.63 | 1.1E-04 | 0.021 |
| V$STAT4_Q4 | Stat4, STAT4, Stat4 | 0.18 | 0.05 | 3.53 | 3.9E-03 | 0.021 |
| V$CEBP_Q2 | CEBPA, Cebpa, Cebpa, Cebpb, Cebpb, CEBPB | 0.18 | 0.04 | 4.23 | 1.6E-03 | 0.022 |
| V$PIT1_Q6 | POU1F1, Pou1f1, Pou1f1 | 0.27 | 0.08 | 3.53 | 5.0E-04 | 0.022 |
| V$LHX3_02 | Lhx3, LHX3, Lhx3 | 0.54 | 0.17 | 3.17 | 5.1E-06 | 0.024 |
| V$IPF1_02 | Pdx1, PDX1, Pdx1 | 0.24 | 0.06 | 4.04 | 4.7E-04 | 0.024 |
| V$IPF1_01 | Pdx1, PDX1, Pdx1 | 0.27 | 0.07 | 4.17 | 1.4E-04 | 0.027 |
| V$STAT5A_Q6 | Stat5a, STAT5A, Stat5a | 0.18 | 0.04 | 5.04 | 6.4E-04 | 0.027 |
| V$IPF1_06 | Pdx1, PDX1, Pdx1 | 0.20 | 0.06 | 3.53 | 2.6E-03 | 0.027 |
| V$ZTA_Q2 | n/a | 0.18 | 0.06 | 3.02 | 8.2E-03 | 0.029 |
| V$RP58_01 | Zfp238, Zfp238, ZNF238 | 0.18 | 0.05 | 3.65 | 3.3E-03 | 0.030 |
| V$PBX1_03 | Pbx1, Pbx1, PBX1 | 0.18 | 0.05 | 3.31 | 5.3E-03 | 0.047 |
| V$AFP1_Q6 | ZFHX3, Zfhx3 | 0.18 | 0.06 | 3.11 | 7.1E-03 | 0.047 |
| Upregulated gene set | Frequency (sites/1000bp) | |||||
| Matrix name | Transcription factor | Up | Background | Ratio | FDR | Matched promoters FDR |
| V$SRF_Q4 | Srf, SRF, Srf | 0.19 | 0.01 | 18.64 | 1.83E-06 | 0.021 |
| V$APOLYA_B | n/a | 0.19 | 0.04 | 4.66 | 2.50E-03 | 0.032 |
| V$TATA_01 | BTAF1, TAF1, TAF10, TAF11, TAF12, TAF13, TAF4, TAF5, TAF6, TAF7, TAF9, Tbp, TBP, Tbp | 0.21 | 0.05 | 4.39 | 2.00E-03 | 0.032 |
| V$OCT4_01 | POU5F1, Pou5f1, Pou5f1 | 0.25 | 0.06 | 4.04 | 1.30E-03 | 0.022 |
| V$TBR2_01 | Eomes, EOMES | 0.25 | 0.06 | 4.04 | 1.30E-03 | 0.032 |
| V$MEF2_05 | Mef2a, MEF2A, Mef2a | 0.21 | 0.05 | 3.97 | 3.30E-03 | 0.035 |
| V$MTATA_B | n/a | 0.42 | 0.11 | 3.67 | 4.44E-05 | 0.002 |
| V$ETS2_B | ELF2, Elf2, ETS1, Ets1, Ets1, ETS2, Ets2, Gabpa, GABPA, Gabpb1, GABPB1, Sfpi1, Sfpi1, SPI1 | 0.23 | 0.07 | 3.44 | 4.50E-03 | 0.049 |
| V$MEF2_03 | Mef2a, MEF2A, Mef2a, Mef2c, MEF2C, Mef2d, Mef2d, MEF2D | 0.25 | 0.08 | 3.09 | 5.70E-03 | 0.041 |
| V$NF1_Q6 | Nfia, NFIA, Nfia, Nfib, NFIC, Nfic, Nfic, Nfix | 0.23 | 0.08 | 3.05 | 7.70E-03 | 0.041 |
The top 100 up- and 100 downregulated genes (query set) were compared to the background set of 1,000 genes with a fold-change ~1. Each row contains information on the performance of one matrix of the positional weight matrix. Average number of putative binding sites per 1,000 base pairs is given for the Up/down regulated genes as well as the background set. The ratio of the two values is provided in the "ratio" column where a number greater than 1 indicates overrepresentation of the motif in the query set. Significance of the representation value is measured by the P value derived from a binomial distribution adjusted with false discovery rate (FDR). "Matched promoters FDR" assesses the statistical significance of the number of promoters in the query set that have at least one predicted site compared to that of promoters in the control set.
Matrix name - tissue factor binding site matrix from TRANSFAC database, Transcription factor - TFs that can bind to the matrix element.
Shown is the data for all matrices with a ratio >3, a FDR < 0.05, and a matched promoter FDR<0.05.